Molecular clones have been isolated and characterized from integrated copies of mouse mammary tumor virus. Only the 3' half of the genome and portions of the 5' half have been successfully cloned. Evidence from our work and from others indicates a small region of the 5' half cannot be cloned in E. coli. Sequence analysis of the extended terminal redundancy of MMTV indicate that potential regulatory signals exist within the E.T.R. Analysis of the regions of host cell DNA flanking the integrated virus fail to reveal any evidence of potential recognition sites for viral integration.